Dear Christoph, Thank for your kind help. My problem was solved after using gromacs-2019.
Best regards, Glenn Christoph Junghans <[email protected]> 於 2023年4月27日 週四 上午12:23寫道： > > > On Tue, Apr 25, 2023 at 19:53 zongyun tsai <[email protected]> > wrote: > >> Dear Christoph, >> The attachment is the error message and lines after adding --verbose >> command. >> > Hmm, we test against gromacs-2023 all the time, but I don’t have enough > experience with macOS and homebrew to help here. > > Two side notes: > 1.) If you want to do coarse-graining you will need gromacs-2019 as > gromacs-2023 doesn’t support tabulated interactions anymore. > 2.) you could try to have votca build its own gromacs version with > -DBUILD_OWN_GROMACS=On. > > Christoph > > >> Sincerely, >> Glenn >> >> Christoph Junghans <[email protected]> 於 2023年4月26日 週三 上午5:20寫道： >> >>> >>> >>> On Tue, Apr 25, 2023 at 00:47 zongyun tsai <[email protected]> >>> wrote: >>> >>>> Dear Christoph, >>>> >>>> My gromacs version is 2023.1, and was built by myself using homebrew. >>>> >>> Can you do a verbose build (add —verbose) and post the error message and >>> lines above again? >>> >>> Christoph >>> >>> >>>> Glenn >>>> >>>> Christoph Junghans 在 2023年4月24日 星期一晚上11:40:24 [UTC+8] 的信中寫道： >>>> >>>>> On Sun, Apr 23, 2023 at 11:26 PM zongyun tsai <[email protected]> >>>>> wrote: >>>>> > >>>>> > Dear Christoph >>>>> > >>>>> > >>>>> > (base) glenntsai@GlenndeAir ~ % cmake --build builddir --parallel 8 >>>>> > >>>>> > [ 1%] Built target csg_inverse_manpage >>>>> > >>>>> > [ 2%] Built target csg_call_build >>>>> > >>>>> > [ 2%] Built target csg_call_manpage >>>>> > >>>>> > [ 2%] Built target csg_inverse_build >>>>> > >>>>> > [ 2%] Built target votca_tools_manpages >>>>> > >>>>> > [ 2%] Built target votca_csg_manpages >>>>> > >>>>> > Current git revision is b533e3901 >>>>> > >>>>> > [ 2%] Built target gitversion >>>>> > >>>>> > [ 17%] Built target votca_tools >>>>> > >>>>> > [ 17%] Built target votca_property >>>>> > >>>>> > [ 17%] Built target unit_test_correlate >>>>> > >>>>> > [ 17%] Built target unit_test_cubicspline >>>>> > >>>>> > [ 19%] Built target unit_test_datacollection >>>>> > >>>>> > [ 19%] Built target unit_test_crosscorrelate >>>>> > >>>>> > [ 19%] Built target unit_test_calculator >>>>> > >>>>> > [ 20%] Built target unit_test_constants >>>>> > >>>>> > [ 20%] Built target unit_test_edge_base >>>>> > >>>>> > [ 22%] Built target unit_test_floatingpointcomparison >>>>> > >>>>> > [ 22%] Built target unit_test_filesystem >>>>> > >>>>> > [ 23%] Built target unit_test_elements >>>>> > >>>>> > [ 25%] Built target unit_test_graphalgorithm >>>>> > >>>>> > [ 26%] Built target unit_test_edgecontainer >>>>> > >>>>> > [ 26%] Built target unit_test_graph_base >>>>> > >>>>> > [ 26%] Built target unit_test_graphdistvisitor >>>>> > >>>>> > [ 26%] Built target unit_test_graph_df_visitor >>>>> > >>>>> > [ 26%] Built target unit_test_graphvisitor >>>>> > >>>>> > [ 28%] Built target unit_test_histogramnew >>>>> > >>>>> > [ 29%] Built target unit_test_graph_bf_visitor >>>>> > >>>>> > [ 31%] Built target unit_test_graphnode >>>>> > >>>>> > [ 31%] Built target unit_test_identity >>>>> > >>>>> > [ 31%] Built target unit_test_name >>>>> > >>>>> > [ 32%] Built target unit_test_objectfactory >>>>> > >>>>> > [ 34%] Built target unit_test_property >>>>> > >>>>> > [ 34%] Built target unit_test_linalg >>>>> > >>>>> > [ 34%] Built target unit_test_optionshandler >>>>> > >>>>> > [ 35%] Built target unit_test_reducededge >>>>> > >>>>> > [ 35%] Built target unit_test_reducedgraph >>>>> > >>>>> > [ 37%] Built target unit_test_structureparameters >>>>> > >>>>> > [ 37%] Built target unit_test_thread >>>>> > >>>>> > [ 38%] Built target unit_test_tokenizer >>>>> > >>>>> > [ 38%] Built target unit_test_table >>>>> > >>>>> > [ 38%] Built target unit_test_random >>>>> > >>>>> > [ 40%] Built target unit_test_akimaspline >>>>> > >>>>> > [ 41%] Built target unit_test_linspline >>>>> > >>>>> > [ 43%] Built target unit_test_unitconverter >>>>> > >>>>> > [ 43%] Built target votca_property_manpage >>>>> > >>>>> > [ 43%] Built target unit_test_NDimVector >>>>> > >>>>> > [ 43%] Built target unit_test_eigenio_matrixmarket >>>>> > >>>>> > [ 43%] Linking CXX shared library libvotca_csg.dylib >>>>> > >>>>> > Undefined symbols for architecture arm64: >>>>> > >>>>> > "read_first_frame(gmx_output_env_t const*, t_trxstatus**, >>>>> std::__1::__fs::filesystem::path const&, t_trxframe*, int)", referenced >>>>> from: >>>>> Hmm, this means something is wrong with the linking against gromacs? >>>>> >>>>> 0.) Do you need gromacs at all? - Otherwise switch it off. >>>>> 1.) What gromacs version are you using? >>>>> 2.) Did you build gromacs yourself? >>>>> >>>>> Christoph >>>>> >>>>> > >>>>> > votca::csg::GMXTrajectoryReader::FirstFrame(votca::csg::Topology&) >>>>> in gmxtrajectoryreader.cc.o >>>>> > >>>>> > "open_trx(std::__1::__fs::filesystem::path const&, char const*)", >>>>> referenced from: >>>>> > >>>>> > votca::csg::GMXTrajectoryWriter::Open(std::__1::basic_string<char, >>>>> std::__1::char_traits<char>, std::__1::allocator<char> >, bool) in >>>>> gmxtrajectorywriter.cc.o >>>>> > >>>>> > "read_tpx(std::__1::__fs::filesystem::path const&, t_inputrec*, >>>>> float (*) [3], int*, float (*) [3], float (*) [3], gmx_mtop_t*)", >>>>> referenced from: >>>>> > >>>>> > >>>>> votca::csg::GMXTopologyReader::ReadTopology(std::__1::basic_string<char, >>>>> std::__1::char_traits<char>, std::__1::allocator<char> >, >>>>> votca::csg::Topology&) in gmxtopologyreader.cc.o >>>>> > >>>>> > ld: symbol(s) not found for architecture arm64 >>>>> > >>>>> > clang: error: linker command failed with exit code 1 (use -v to see >>>>> invocation) >>>>> > >>>>> > make[2]: *** [csg/src/libcsg/libvotca_csg.2024.dylib] Error 1 >>>>> > >>>>> > make[1]: *** [csg/src/libcsg/CMakeFiles/votca_csg.dir/all] Error 2 >>>>> > >>>>> > make: *** [all] Error 2 >>>>> > >>>>> > >>>>> > >>>>> > Glenn >>>>> > >>>>> > >>>>> > Christoph Junghans 在 2023年4月24日 星期一上午11:51:51 [UTC+8] 的信中寫道： >>>>> >> >>>>> >> On Sun, Apr 23, 2023 at 19:38 zongyun tsai <[email protected]> >>>>> wrote: >>>>> >>> >>>>> >>> Hello, >>>>> >>> I encountered an Error message while when running the following >>>>> command: >>>>> >>> cmake --build builddirThe error shown in the terminal states that >>>>> >>> >>>>> >>> clang: error: linker command failed with exit code 1 (use -v to >>>>> see invocation) >>>>> >> >>>>> >> can you post the lines above this error? >>>>> >> >>>>> >> Christoph >>>>> >>> >>>>> >>> make[2]: *** [csg/src/libcsg/libvotca_csg.2024.dylib] Error 1 >>>>> >>> >>>>> >>> make[1]: *** [csg/src/libcsg/CMakeFiles/votca_csg.dir/all] Error 2 >>>>> >>> >>>>> >>> make: *** [all] Error 2 >>>>> >>> >>>>> >>> Can you please suggest some ways to correct this error? >>>>> >>> Thank you,Glenn >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> -- >>>>> >>> Join us on Slack: https://join.slack.com/t/votca/signup >>>>> >>> --- >>>>> >>> You received this message because you are subscribed to the Google >>>>> Groups "votca" group. >>>>> >>> To unsubscribe from this group and stop receiving emails from it, >>>>> send an email to [email protected]. >>>>> >>> To view this discussion on the web visit >>>>> https://groups.google.com/d/msgid/votca/60a4e6f3-51d2-49a2-ad60-5b6df3d064d2n%40googlegroups.com. >>>>> >>>>> >> >>>>> >> -- >>>>> >> Christoph Junghans >>>>> >> Web: http://www.compphys.de >>>>> > >>>>> > -- >>>>> > Join us on Slack: https://join.slack.com/t/votca/signup >>>>> > --- >>>>> > You received this message because you are subscribed to the Google >>>>> Groups "votca" group. >>>>> > To unsubscribe from this group and stop receiving emails from it, >>>>> send an email to [email protected]. >>>>> >>>> > To view this discussion on the web visit >>>>> https://groups.google.com/d/msgid/votca/3db772b3-1c44-4dad-ae1c-edea78357445n%40googlegroups.com. >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Christoph Junghans >>>>> Web: http://www.compphys.de >>>>> >>>> -- >>>> Join us on Slack: https://join.slack.com/t/votca/signup >>>> --- >>>> You received this message because you are subscribed to the Google >>>> Groups "votca" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to [email protected]. >>>> To view this discussion on the web visit >>>> https://groups.google.com/d/msgid/votca/2d28cdcd-9b3f-4d75-9dd8-f54ca7319e81n%40googlegroups.com >>>> <https://groups.google.com/d/msgid/votca/2d28cdcd-9b3f-4d75-9dd8-f54ca7319e81n%40googlegroups.com?utm_medium=email&utm_source=footer> >>>> . >>>> >>> -- >>> Christoph Junghans >>> Web: http://www.compphys.de >>> >>> -- >>> Join us on Slack: https://join.slack.com/t/votca/signup >>> --- >>> You received this message because you are subscribed to the Google >>> Groups "votca" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to [email protected]. >>> >> To view this discussion on the web visit >>> https://groups.google.com/d/msgid/votca/CAHG27e4ZtqYZdBbsw4QpOZ5pZhKgawrJxs3Qqnn3Wov%3DqQ2wKw%40mail.gmail.com >>> <https://groups.google.com/d/msgid/votca/CAHG27e4ZtqYZdBbsw4QpOZ5pZhKgawrJxs3Qqnn3Wov%3DqQ2wKw%40mail.gmail.com?utm_medium=email&utm_source=footer> >>> . >>> >> -- >> Join us on Slack: https://join.slack.com/t/votca/signup >> --- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/CAJs%3DatKxwXn563-bqJ_CPKOdDmqB9z_5ZkFymXX-AGoQ5tGS2A%40mail.gmail.com >> <https://groups.google.com/d/msgid/votca/CAJs%3DatKxwXn563-bqJ_CPKOdDmqB9z_5ZkFymXX-AGoQ5tGS2A%40mail.gmail.com?utm_medium=email&utm_source=footer> >> . >> > -- > Christoph Junghans > Web: http://www.compphys.de > > -- > Join us on Slack: https://join.slack.com/t/votca/signup > --- > You received this message because you are subscribed to a topic in the > Google Groups "votca" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/votca/Rs14o7iLiiY/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAHG27e7E8B4mQf7K4dJX5SBsXbmTbNaFM-u9%3Dx76LG%2Ba4XFgMQ%40mail.gmail.com > <https://groups.google.com/d/msgid/votca/CAHG27e7E8B4mQf7K4dJX5SBsXbmTbNaFM-u9%3Dx76LG%2Ba4XFgMQ%40mail.gmail.com?utm_medium=email&utm_source=footer> > . > -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAJs%3DatL%3DcYzG7VMiAsObg0c1SvZxLDbFD5m5ZJ9Jpp%3DPCizdEg%40mail.gmail.com.
